SNP Detail Info-rs2393938

Sequence Name	Change(s)
GRCh38.p7 chr 10	NC_000010.11:g.43568364T>C
GRCh37.p13 chr 10	NC_000010.10:g.44063812T>C

Molecule type	Change	Amino acid[Codon]	SO Term
ZNF239 transcript variant 2	NM_001099282.1:c.	N/A	Intron Variant
ZNF239 transcript variant 4	NM_001099283.1:c.	N/A	Intron Variant
ZNF239 transcript variant 3	NM_001099284.1:c.	N/A	Intron Variant
ZNF239 transcript variant 5	NM_001324347.1:c.	N/A	Intron Variant
ZNF239 transcript variant 6	NM_001324348.1:c.	N/A	Intron Variant
ZNF239 transcript variant 7	NM_001324349.1:c.	N/A	Intron Variant
ZNF239 transcript variant 8	NM_001324350.1:c.	N/A	Intron Variant
ZNF239 transcript variant 9	NM_001324351.1:c.	N/A	Intron Variant
ZNF239 transcript variant 10	NM_001324352.1:c.	N/A	Intron Variant
ZNF239 transcript variant 11	NM_001324353.1:c.	N/A	Intron Variant
ZNF239 transcript variant 1	NM_005674.2:c.	N/A	5 Prime UTR Variant
ZNF239 transcript variant X9	XM_006718003.3:c.	N/A	Intron Variant
ZNF239 transcript variant X1	XM_011540232.2:c.	N/A	Intron Variant
ZNF239 transcript variant X2	XM_011540234.2:c.	N/A	Intron Variant
ZNF239 transcript variant X3	XM_011540235.2:c.	N/A	Intron Variant
ZNF239 transcript variant X5	XM_011540236.2:c.	N/A	Intron Variant
ZNF239 transcript variant X6	XM_011540237.2:c.	N/A	Intron Variant
ZNF239 transcript variant X4	XM_017016740.1:c.	N/A	Intron Variant
ZNF239 transcript variant X8	XM_005271832.2:c.	N/A	Genic Upstream Transcript Variant
ZNF239 transcript variant X7	XM_006718001.2:c.	N/A	Genic Upstream Transcript Variant
ZNF239 transcript variant X10	XM_011540238.2:c.	N/A	Genic Upstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.852	C=0.148
1000Genomes	American	Sub	694	T=0.790	C=0.210
1000Genomes	East Asian	Sub	1008	T=0.554	C=0.446
1000Genomes	Europe	Sub	1006	T=0.845	C=0.155
1000Genomes	Global	Study-wide	5008	T=0.775	C=0.225
1000Genomes	South Asian	Sub	978	T=0.820	C=0.180
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.871	C=0.129
The Genome Aggregation Database	African	Sub	8706	T=0.830	C=0.170
The Genome Aggregation Database	American	Sub	838	T=0.770	C=0.230
The Genome Aggregation Database	East Asian	Sub	1612	T=0.551	C=0.449
The Genome Aggregation Database	Europe	Sub	18486	T=0.866	C=0.133
The Genome Aggregation Database	Global	Study-wide	29944	T=0.836	C=0.163
The Genome Aggregation Database	Other	Sub	302	T=0.850	C=0.150
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.834	C=0.165
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.874	C=0.126

PMID	Title	Author	Journal
20158304	A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.	Lind PA	Twin Res Hum Genet

SNP ID	p-value	Traits	Study
rs2393938	7.13E-06	alcohol and nictotine co-dependence	20158304

eQTL of rs2393938 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr10:44063812	ZNF239	ENSG00000196793.9	T>C	1.5066e-7	-6254	Cerebellum
Chr10:44063812	ZNF239	ENSG00000196793.9	T>C	2.3808e-4	-6254	Cortex
Chr10:44063812	ZNF239	ENSG00000196793.9	T>C	1.1330e-3	-6254	Cerebellar_Hemisphere
Chr10:44063812	ZNF239	ENSG00000196793.9	T>C	1.9226e-2	-6254	Caudate_basal_ganglia

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr10	44068463	44068676	E067	4651
chr10	44068686	44068740	E067	4874
chr10	44068354	44068429	E068	4542
chr10	44068463	44068676	E068	4651
chr10	44068686	44068740	E068	4874
chr10	44102909	44102959	E068	39097
chr10	44102981	44103031	E068	39169
chr10	44068463	44068676	E069	4651
chr10	44068686	44068740	E069	4874
chr10	44102909	44102959	E069	39097
chr10	44102981	44103031	E069	39169
chr10	44068463	44068676	E071	4651
chr10	44068686	44068740	E071	4874
chr10	44091003	44091153	E071	27191
chr10	44102909	44102959	E081	39097
chr10	44102981	44103031	E081	39169
chr10	44068354	44068429	E082	4542
chr10	44102909	44102959	E082	39097
chr10	44102981	44103031	E082	39169

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr10	44068743	44070477	E067	4931
chr10	44101444	44102892	E067	37632
chr10	44068743	44070477	E068	4931
chr10	44101444	44102892	E068	37632
chr10	44068743	44070477	E069	4931
chr10	44101444	44102892	E069	37632
chr10	44068743	44070477	E070	4931
chr10	44101444	44102892	E070	37632
chr10	44068743	44070477	E071	4931
chr10	44101444	44102892	E071	37632
chr10	44068743	44070477	E072	4931
chr10	44101444	44102892	E072	37632
chr10	44068743	44070477	E073	4931
chr10	44101444	44102892	E073	37632
chr10	44053211	44053261	E074	-10551
chr10	44068743	44070477	E074	4931
chr10	44101444	44102892	E074	37632
chr10	44068743	44070477	E081	4931
chr10	44101444	44102892	E081	37632
chr10	44068743	44070477	E082	4931
chr10	44101444	44102892	E082	37632

rs2393938